Bruce Schneier has some test vectors for the algorithm on his site. You could write some tests to verify your usage. Whenever docs are not explaining how to use a function its best to download the source and view the tests and those will show you how to use it. The mcrypt extension tests actually uses Schneier's vectors. See ./php-5.4.9-src/ext/mcrypt/tests/blowfish.phpt

As for transmitting and receiving data just make sure keep an eye on encoding, the web stack tends to be loose and wild with it, that is character encoding, server-side gzip and so on. You may want to put in checks to make sure outdated versions of SSL/TLS are not being used. As for communicating with a shared server, you may want to include checks on where you put your data, make sure the file or database doesn't have shared or group read permissions, make sure not to use temporary directories as they can be shared locations, use secure network connection to the database, et cetera.